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Sample GSM368183

Query DataSets for GSM368183

Status

Public on Feb 07, 2009

Title

NPC sample from patient2 (male)

Sample type

SRA

Source name

Nasopharyngeal Carcinoma

Organism

Homo sapiens

Characteristics

tissue: undifferentiated NPC

Treatment protocol

clinical dissection, frozen samples.

Extracted molecule

total RNA

Extraction protocol

From all samples, RNA species smaller than 200 bases were enriched with the mirVana miRNA isolation kit (Ambion, Austin, Texas, USA). The small RNAs from all 4 samples were separated on a denaturing 12,5% polyacrylamide (PAA) gel and stained with SYBRgreenII. As molecular mass standard a mixture of oligonucleotides was used that range in size between 15 and 30 bases. The population of miRNAs with a length of 15 – 30 bases was obtained by passive elution of the RNAs from the gel. The miRNAs were then precipitated with ethanol and dissolved in water. For cDNA synthesis the RNAs were first poly(A)-tailed using poly(A) polymerase followed by ligation of a RNA adapter to the 5´-phosphate of the miRNAs. First-strand cDNA synthesis was then performed using an oligo(dT)-linker primer and M-MLV-RNase H- reverse transcriptase. The resulting cDNAs were then PCR-amplified to about 20 ng/μl using the high fidelity polymerase Phusion (Finnzymes). The fusion primers used for PCR amplification were designed for amplicon sequencing according to the instructions of 454 Live Sciences. Barcode sequences for each cDNA species are attached to the 5'-ends of the cDNAs. cDNAs of 4 samples were mixed in equal amounts. The correct size range was obtained by separation of the mixed cDNAs on and electroelution of the 120 – 135 bp fraction from 6% PAA-gels followed by purification of the eluted cDNAs using Nucleospin Extract II (Macherey and Nagel). The cDNAs were pooled (Volume: 30 μl; Concentration: 13 ng/μl; dissolved in 5 mM Tris pH:8,5) and sent for 454 sequencing. Small RNA cloning was performed by Vertis Biotechnologie AG (Weihenstephan, Germany)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

454 GS 20

Description

Total endogenous small RNAs between 15 and 30 bases from NPC sample of patient2

Data processing

Processed data file contains the reads with 5' and 3' adapters removed. Same reads are sorted together and the numbers of repetitivity are illustrated

Submission date

Feb 06, 2009

Last update date

May 15, 2019

Contact name

Gunter Meister

E-mail(s)

meister@biochem.mpg.de

Organization name

Max Planck Institute of Biochemistry

Department

Center for Integrated Protein Science Munich (CIPSM)

Lab

RNA Biology

Street address

Am Klopferspitz 18

City

Martinsried

ZIP/Postal code

82152

Country

Germany

Platform ID

GPL9178

Series (1)

GSE14738

Identification of novel Epstein-Barr Virus miRNA genes from Nasopharyngeal Carcinomas

Relations

SRA

SRX012423

BioSample

SAMN00004753

Data table header descriptions
SEQUENCE
COUNT	counts

Data table
SEQUENCE	COUNT
AAAAAAAAAAAAAAAAAGTTGCCCTCGGCTT	1
AAAAAAAAAAACTAAGGTGGCGTGTGACAGCGGCTG	1
AAAAAAAAAAACTAGGAAAGTGGATGGCGCTGG	1
AAAAAAAAAAACTTAGGACCGCTCTGCC	1
AAAAAAAAAAAGAAACGTGGCGCTGCGGATG	1
AAAAAAAAAACGTAACGGCGGCGCGCGTACCGCTGG	1
AAAAAAAAAATAAAAAAAAAGAAACGGCGACGGAG	1
AAAAAAAAAATAAAAAAGAGTATGTTTGATATATT	1
AAAAAAAAAATAAGGAGGTAGTAGGTTGTATAGT	1
AAAAAAAAACTTGGCTGTCACTC	1
AAAAAAAAATAGGTGGCGTCGGAGGGCGGCG	1
AAAAAAAACCGGACGGCTTTGGTGACTCTAGAT	1
AAAAAAACGACTGAGAAGACGGTCG	1
AAAAAAAGACTGGGTTGAGNGGGAACG	1
AAAAAAAGAGACATGAGAGGTGT	1
AAAAAAATAAAAGCCGTGGCGGCCGTAGCGC	1
AAAAAAATAAAGCCGTGGCGGCCTTAGCGC	1
AAAAAAATTGAGTTGTGAACAAATG	1
AAAAAAGAACTACGATTGTCTGCTGGGTT	1
AAAAAAGCGTGGGTTGAGGAGGGAAAAAAAAACG	1

Total number of rows: 13112

Table truncated, full table size 310 Kbytes.

Supplementary data files not provided

SRA Run Selector

Processed data included within Sample table

Raw data are available in SRA